Master Naruto
by Forever Rahhel
Summary: Naruto Doctor Who crossover. Instead of hiding himself at the end of the universe the Master turns himself into a human and escapes to the Narutoverse. The human he is posing as is...Uzumaki Naruto NarutoxYugito
1. Prologue

**Disclaimer: I'm Masashi Kishimoto and I have realized, that my actual manga is too Sasuke centric therefore I write this fic in order to correct my mistakes I have done in the manga...not.**

Naruto Doctor Who crossover. Instead of hiding himself at the end of the universe the master turns himself into a human and escapes to the Narutoverse. The human he is posing as is...Uzumaki Naruto NarutoxYugito

**A/N: Yes, I know I should finish my other stories, but inspiration is really fickle and I wouldn't mind, if other authors would pick up my other pieces, but on the other hand I will finish them within the timespan that it my life anyway.**

**Warning this story hasn't seen a beta, it may cause your eyes to bleed because of grammar errors and plot holes.**** Any volunteers are appreciated. For contact look at my profile.**

_**Master Naruto **_

**Prologue: I...AM...THE...MASTER**

Once again he finds himself at the ramen stand Naruto loves so much. The owner and his daughter were always kind to him and the meals were cheap and filling, but this time the bitter taste of failure was too strong to be washed over by his beloved ramen. The reason for his bitterness was the third failure in the Genin examination. He is now 15 years old and nothing learnt, but to throw shuriken, kunais and do some cheap parlor tricks, that are called Ninjutsu. All he has left are the clothes he is wearing and the broken fog watch he has since the day he was born. Being an academy student for Konoha's military filled his stomach and gave him a place to live. Now, that he is no longer a part of the program he is left with nothing. Every students receive a stipendiary in order to live for themselves, this also applys to students with families and clans.

Too make it worse those sounds in his head were getting louder and louder, there were voices at times calling out to him as it seemed, but the only constant, which remained was the sound of drumming.

**Tak Tak Tak...Tak Tak Tak **

This constant drumming was driving him into madness and it also seemed like as if the sounds and voices got louder when he exams the fob watch. This fog watch was a mystery to him. He was found with it...an orphan after the wake of the Kyuubi no Youko. The signs on the fog watch didn't match any language the village has seen. Even an extended visit to the library was proven futile and so was the visit of the Sandaime Hokage, who was after all known as the professor was at a loss. No one was able to open it and he never tried it himself, because something in his head told him it was broken.

"...uto Naruto, listen to me. We are closing in 20 minutes. You should eat up." The sound of the owner's daughter got him out of his mind set. She was a petite girl around Naruto's age. Her looks were probably one of the reason for the good business of th small ramen stand. Many men love that innocent girl in a white outfit style she exhibited. Her gentle smile encouraged people and she had always an open ear for the guests and especially for Naruto. People say she had a weakness for the smart blond...

People would wonder why someone who is considered smart would fail the Genin exam thrice. The answer is simple...Bunshin no Jutsu. It is an illusionary manifestation, which is created by using the chakra of the user to break the light and creating a mirage, which looks like the user him- or herself. Naruto had no problem to understand the concept to be quite frankly he was the one who found out this very truth. He revealed this to the Sandaime, who confirmed this after he checked it out himself. Naruto was considered a genius, because of this discovery, but even geniuses have to go through the standard procedure, which is creating at least three Bunshin. For some odd reason it wasn't possible for him to do it. His chakra seemed to have a life on its own and the minor breaking of light is not enough for it to obey the will of its master. Chakra control itself is relative value. You could have twice the amount of chakra control of Kakashi Hatake, but still suck at medic Ninjutsu. The nature of chakra is different in each individual; it can be malevolent of uncontrollable wild like in Naruto's case.

"Sorry, what did you say, Ayame?" The brown haired girl looked at him with a frown and sighed.

"Geez Naruto, you always space out. You think too much. One day you might miss your whole life, if you waste it on thinking too much. In any case, I asked you what that thing is you keep playing with. It looks like some kind of cursed object." Even when she criticizes someone she doesn't loose the innocent girl next door air around her.

"This?" He stretches out his hand revealing the fob watch to her. "This is a fob watch."

"Oh, that looks quite antique, can you open it?" Her curiosity was obviously woken up by this. Not only those this item involve Naruto, but it is also antique, which makes it all the more interesting for her.

"Ohh no, it's old and broken. It's not meant to be...I never tried to open it." His eyes have turned hazy as if hypnotized by the watch.

"How would you know, if it is broken if you never tried to open it in the first place?" Her curiosity was at its peak, but it seemed like fate intervened, because her father shouted from the kitchen to start closing the stand. Little did she know, that this little event prevented her to be witness of a new master above all masters.

* * *

**Naruto's home at night**

Naruto was sitting on his bed unable to sleep. Not only has the volume of the drums increased, but now familiar voices are screaming at him. They are demanding him to open to fob watch. The feeling of utter depression caused by his failure still hasn't vanished and its nagging at him along with the voices.

_**...Time Lord...TARDIS...Regeneration...Muhahaha... the drums, the drums, the never ending drum beat open me you human fool; open the light and summon me and receive my majesty...destroy it! And you will give part to me...** _

That does it. Those voices were commanding him to open him. What could happen at worst? The watch doesn't seem as breakable as other antiques and has so far withstood any kind of treatment it received during Naruto's training. Yes, he pushed the button and white light flew out into him. The light was blinding for everyone, who could have stood around here, but this was not the case. Revelation started to cross his eyes. His eyes seemed to gain knowledge of several hundreds of years, if not more. The light has...enlightened him, to say the least. All the knowledge he once possessed is once again his at his disposal.

The memories of his life as Naruto intermingle with the life experience of his former self. This former self ,totally overwhelms the old life of Uzumaki Naruto and the only one who remains is the old being in a black standard uniform for upcoming ninjas. No longer are the voices shouting at him instead the future of this planet unfolds itself in front of his eyes. Past, present and future are no secret to him. His knowledge is unrivaled and no one is there to stop him...but what is this feeling he has in his guts...it seems familiar like his old arch rival, but still different.

* * *

**In a dark cave at a statue **

A pull was felt by an individual in this cave. A pull he hasn't felt in years. He is known as the mentor of the most sought out missing Nin in Konoha's history and also as the numb skull of a certain organization. He is covered in black gear and hides his face under a mask with one eye hole. In an earlier life he was one of the mightiest persons in the universe and someone who thinks outside the box, despite the fact he once lived in a box. He knows, this feeling in his gut could only mean one thing...

"It seems like as if I'm not the only survivor after all. This world may prove more interesting than I suspected earlier, but where have I sensed this presence before?"

All he could do is wait, even if all Time Lords had the ability to look into the future, they are far off from being omniscient, because other Time Lords and individual choices make the time line unpredictable to a certain extent.

* * *

**"I-AM-THE-MASTER-REBORN-"**

"The Master" is a name he has chosen himself after graduating from the Time Lord academy. His aim is to become the master of all matters. In this new world without his arch rival The Doctor and the other Time Lords his plans won't be foiled by anyone. Resistance is futile. This world doesn't know what will await them. With their lack of brains they can't stop him. All the technology they have acquired are for entertainment purposes only. He could simply overpower them with laser beams or even projectile weaponry. He always thought the earthlings to be apes, but if those people in his universe were apes then the humans here are ants. Yes, ants is the right term. They are physically strong, but can't think for themselves.

All he needs is hear in this apartment. Not only was he found with the fob watch, but there was also this grandfather clock. Heh, a watch first and a clock now. Everything is connected with time, how appropriate for a Time Lord. Not only was the so called perception filter applied to the chameleon arc. The chameleon arc is a device that reverses the biology of a Time Lord and changes him into a human. No one would suspect this watch to be that complex. The Grandfather clock fulfills the same function as the watch. It is supposed to distract the people from its true purpose. It is a TARDIS; a time machine.

This shall be the begin of my journey to mastery over everything! And the so called Kyuubi sealed in side him, will help whether it wants to or not...after all pet with out a master is not much of an pet.

"**Muhahaha!"**

* * *

**A/N: Okay this shall be the prologue for my crossover. This will be one of my serious fics, so I have a 50 ratio between humor and non-humor fics. Please don't bitch about me not updating my stories. I either don't have any inspiration for that story, lack of time or I just don't feel like writing at the moment. Well, what else can I say, I hate Kishimoto for raping Itachi's personality and making the Sharingan into the Marysuegan. At the moment I have exams, so updating will be slow. I could say slower than usual, but that's not possible in my case. Also fanfiction annoys me a lot with their recent changes. I mean they could let us choose if we want to use lines of that border things from StarOffice. Another new things which pisses me off is the new way of posting in the forums. It's a pain in the ass to make proper paragraphs now that after pressing the enter button the cursor jumps over a line.**

**Something else which is annoying is that they still haven't added Yugito into the character search bar. I mean come on. She was in as much chapters as Yugao and she is the search bar. **

**Also authors like Zagger of Giovanni have a hard time advertising their fics outside of forums and C2's. Check out my profile to get to Zagger's forum in order to gain decent access to Yugito fics. You won't find all of them, but you will find the most popular and under-rated once. Please send emails to fanfiction to get them to add Yugito into the character search bar and please do it properly. Don't just say it in a one sentence, but elaborate how important she is.**

**This will be added under Naruto/Kyuubi, because of said problem and it will be quite important in the future. **

**29th April 2008**


	2. c1 I am The Master and you, will obey me

**Claimer: I finally ceased control over Naruto the manga and anime. **

**Naruto Doctor Who crossover. Instead of hiding himself at the end of the universe the master turns himself into a human and escapes to the Narutoverse. The human he is posing as is...Uzumaki Naruto NarutoxYugito**

**A/N: Hmm, I actually updated. This counts as Christmas miracle for you guys, despite the fact it's New Year.**

**Warning this story hasn't seen a beta, it may cause your eyes to bleed because of grammar errors and plot holes. Any volunteers are appreciated. For contact look at my profile.**

_**Master Naruto **_

**Chapter one: I am The Master and you, will obey me!**

"Raikage-sama!"

The voice rang in the office of the current Kage of Kumogakure no Sato. No one knew the Kage very well despite the fact that he won in the "election" three years ago. This so called "election" wasn't much of an election, if you believe the rumors cycling around the Land of Lightning. His predecessor vanished without a trace and all the possible candidates were either involved in scandals or withdrew their candidacy stating no reason whatsoever. Those two facts were mighty suspicious, but there was no other choice left, but to elect the remaining candidate The Land of Lightning would be vulnerable to the other major nation without their second king. The daimyo alone was powerless and the Kage on their own was almighty. Such a faulty system.

"Stand up, my dear."

She was the only person in this village who was called that by him. The villagers suspected a hidden romance, but the ninjas of Kumogakure knew better. Such a title was only reserved for the most loyal follower of their knew Kage. It wasn't a therm of endearment, but an honoury title. A title only one person would ever receive.

"Yes, sir!"

The woman kneeling in front of her lord stood up. She made even such a simple act look graceful. Not even Geishas could move in such ways as she did. In more than one way she is like a feline. Beautiful to look at, but woe to the one who provokes her! Her claws are as sharp as on of the legendary swords of legends. Here long blond hair was bound into a Chinese Pigtails hold by a white bandage. A sure sign for her commitment to her job. Her green eyes were slanted not unlike that of her Kage. It gave them both a wild look, but while her pale skin made her look like a vengeful ghost his tanned skin gave him a demonic appearance. The only thing that made her stand out from ever shinobi is her fire red dress. It wasn't skimpy by any standard, but it just screamed seduction. If she wouldn't be known by the whole village she would be mistaken for one of the noble women, who diligently took care of themselves to look like goddesses.

"Talk!" Came out the voice of the leader. He was never much of a talker it seemed, but the truth is he only talked a lot when it was necessary to accomplish a goal. Smooth talking was one of his lesser abilities. I was also one of the few known once. No one has ever seen him fight. To have such a mysterious individual as your leader was truly a surprise. To think that such an important position was entrusted to an virtually unknown person was unheard of.

"Message from Iwagakure arrived. Deidara-san lead the so called terrorist organization to a victory. He is officially the Godaime Tsuchikage. Iwagakure signed the treaty as planned. "

"Excellent my dear. With this development, most of Konoha is cut off from the north. Hehehe" The laughter of the Raikage rang through the room. His laughter was unmistakable. No one could imitate it. It was dark, so dark and malicious most of the people were deadly afraid of him. It gave him a dark charm though that many women have fallen for.

"What about Kusa and Taki, my lord?" Such an exchange wasn't a rarity for her. She always knew he wouldn't answer her completely. Sometimes he would speak in riddles on others he would only reveal snippets of the whole story. It never ceased to amaze her how smart her new leader was. In a period of a year any kind of resistance was crushed mercilessly; like a real ninja he back stabbed, tortured, maimed and he did it beyond the knowledge of the civilians. For the first time in nearly 67 years a real ninja was in power. Wannabe ninjas like the once created in Konoha had no chance. Considering the fiasco three years ago it's a miracle they survived so long. Without Danzou talking over the village there existence would have diminished on that time.

"Taki was annexed by Iwa after a severe bombing and Kusa was taken over by Ame. No one knows what they are up to, but I have an idea what will happen or more precisely what has happened. Their leader is a formidable foe. Once he was my arch enemy he likes to be known as...."

Once again he sat on his throne. In this country he has conquered, he is king. The only king. His plans so far were on the right course. The only obstacle in his master plan is Uchiha Itachi. The renegade Uchiha is a formidable opponent even with everything he has learnt, he still couldn't defeat him. What he needed was an ally, a strong ally, but who? Iwagakure, Kirigakure and Amegakure are out of the question. The strongest ninja villages now was Kumogakure. Konoha itself was in better shape than all the other major villages. The attack three years ago had not the desired effect. Instead of succumbing to the chaos, created by the invasion and the death of their Kage, he was replaced by a stronger Hokage. His ninja skills were actually not any better than that of any Chunin, no, what made him stronger is leadership and the ability to see what a ninja truly was, a weapon. Danzou made Konoha strong again. No longer were they the laughing stock among the real ninjas. An alliance would be beneficial, but the chances were close to nil. With his reign they adopted an unforgivable policy. No longer was it possible for missing nin to crawl back and expect mercy. Konoha was no option for him.

Kumogakure on the other hand is hard to calculate. The new leader was probably just as strong politically as Danzou, if not even stronger. His spy network hasn't come up with anything useful. How is he supposed to plot without any information?

" 'Sasuke-kun' "

Ah, the blond Kunoichi was always speaking his name in that tone. That tone was always sarcastic, but still amused. Persuading her to follow him was easier than expected. She was the only one who was his age. Well, mentally that is.

"Kukukukuku, what is it Tsunade-hime?"

"We have received an offer from an old friend. I believe the message brought by this 'Sai' is something you have waited for. " That amused smile didn't vanish for even one second since she started speaking. She seemed to be happy. On the other hand she was always happy nowadays.

"Hn, bring him in Kabuto-kun!" Kabuto was always the one to deliver important messages or prisoners. He and Tsunade were his most trusted companions. His only companions. Everyone else were followers or sheeps ready to be sacrificed when necessary.

Kabuto entered the throne room holding a pale, black haired boy. The boy was obviously one of Danzou's ROOT ninjas. Those were the elite ninjas who have served him for years. They always looked the same. Remaining in the shadows had its toll on their skin.

"Tell me Sai-kun, what is that your master has to offer me?"

"I'm only the delivery boy, Sasuke-sama. Everything will be explained on this scroll." He draws out a scroll slowly. Smart boy doesn't want to give the wrong impression. Handing over the scroll first to Kabuto to check for eventual traps. It wouldn't be the first time Danzou killed a noble or a leader of an opposing fraction with trickery.

Kabuto handed over the scroll to Sasuke after a thorough check. The content intrigued Sasuke. This would solve the problem of finding an ally. Some deity must like him. This could be his chance to accomplish his goal and turn an enemy to his ally. Permanently.

"Tell Danzou-dono I accept his offer. We may discuss this further on the border of Rice country and Fire county, personally. Tsunade-hime, would be so kind to show Sai-kun the exit?"

Tsunade obliged without any question. As a companion she was free to do as she likes. She wasn't under his command. It doesn't matter. What he gave her ensured her loyalty to him. Women were so complicated and simple at the same time. What an oxymoron. And people wondered why he was never seen with female company during his lifetime in Konoha.

"Orochimaru-sama."

He was torn out of his thought process by his most loyal companion. "Kabuto-kun, how many times have I told you not to call me that anymore. The world is supposed to presume me dead."

The only thing he received from him was his cocky smirk. It made Orochimaru sigh. Sometimes he wondered why he bothered with him. He will never understand him. Such a childish boy, but still amusing. He was the only one who could amuse him at times like these.

Apparently it was a tradition to have a nickname, when you became an outstanding ninja. The blond was never a fan of those nicknames. For a ninja fame shouldn't exist and for a being such as himself he would have embraced the fameless occupation of a ninja, but alas ninjas in this world were popularity whores to say the least and even he got a nickname to his utter dismay. The Last. A strangely fitting name for him. Even though there was another, but in time he will truly become the last of his kind.

"And another prediction of mine has become a fact. What a surprise." Was the statement of the Timelord.

"We may ask your companion to follow us. Resistance is futile." The monotone voice belonged to the legendary Uchiha known as Itachi The Kin Slayer. Confronting him alone would be less of a hassle, if it wouldn't be for his partner. A very few knew this character, because he is probably the oldest human on this planet. This was Naruto's second encounter with him. The first time they met he was under the disguising himself as the Shodai Hokage. The Jinchuuriki would kick himself for being so careless back then. This man in front of him known as The Shylock stole one of his hearts. Without that extra heart a great deal of his power diminished. It also came with one advantage. He couldn't be detected anymore, neither by Timelords nor by Daleks.

"I'm afraid, but I can't let you have Yugito. She is a very important person to me, but fear not she will see you again when she crushes your puny organization as you like to call it."

"I see, so you leave no other choice, but to force you into submission. Kakuzu, you will take care of her, while I do my job."

"Tse, I don't have any use for the Raikage anyway. There is not even a bounty on his head. Quite disturbing, I have never heard of a Kage without a bounty." Yugito who stood still and remained silent during this exchange made herself ready to take on the loan shark. Her motivation was to protect the only one in this world who appreciated her. It may only be for her strength or skill, but sometimes Naruto seemed to show her that he values her more than a potential weapon. A comforting thought.

Both Yugito and Kakuzu were engaged into a physical fight, while both the Kage and Itachi stood still gazing into each others eyes. Those two were known in their world for their ability to manipulate people with their eyes. Today will show them whose eyes are more hypnotic.

"Your will against mine? So be it." The red slitted eyes bores themselves into the windmill of the Sharingan.

**A/N: I know it's way too short for a chapter plus I made it end on a cliffhanger, but I just can't find any inspiration. I'm not going to abandon any of my fics, but I wouldn't mind, if any one would pick them up for me. I'm now in a college for foreign language correspondents, which is way harder than I expected. Luckily my schedule mostly consists of English and Economics. I hate interpreting. I'm definitely going to do just some casual translating. It's way easier, stress free and I can take my time. **

**Coming back to fanfiction. I decided to upload in a snippet of another idea I had. I'm probably not going to post it or maybe I'm going to post it under Naru/Sasu just to see what happens. Silly fangirls will think it's yaoi, but you people will know better. The story will be known as "Fall of an angel". It will be under the Naru/Kyuu section and the same story will be posted under the Naru/Sasu for great justice under a different name....hmmmm why shouldn't I call it "For great justice"**


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